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PDB:2ic8

Protein Name

Rhomboid Protease GlpG

Species

Escherichia coli

Biological Context

A serine protease active in the cell membrane

GlpG is a kind of hydrogenase (EC 3.4.21.105) belonging to the rhomboid protease family, but yet an integral membrane protein derived from Escherichia coli inner membrane. The protein is composed of several transmembrane helices, on which the active site residues are situated. Although one may also call it serine protease because its active sites contain Ser and His, its structure composed of only alpha-helices embedded in the membrane is completely different from typical serine proteases (e.g., trypsin) having folds of the all-beta type. Rhomboid-proteases are widely distributed across prokaryotes to eukaryotes, and play various roles in different species. For instances, Rhomboid-1 from fruit fly regulates epidermal growth factor (EGF) receptor signaling by cleaving the transmembrane domain of Spits, the principle ligand of the EGF receptor. Human homolog PARL regulates cytochrome c release during apoptosis. The X-ray structure of GlpG answered a question how hydrolysis reaction can take place in non-aqueous environment of the membrane lipid bilayer.

Structure Description

2ic82ic8_x2ic8_y

Of six transmembrane helices (S1 – S6) of GlpG, the S4 helix does not pierce through the membrane, but one of the helical ends (i.e., N-terminus) remains about 10 A below the membrane surface (Fig. 1). This makes a cavity within the lipid bilayer of the membrane, and the cavity is open towards the extracellular milieu so as to make its inside hydrophilic (Figs. 1 and 2). Two helices, S1 and S2, are connected with a relatively long loop (L1) composed of 27 residues, which contrary to our expectations is embedded in the membrane (Figs. 1 and 2). Both of these structural features are significant for the enzymatic function as follows. Active site residues, Ser-201 and His-254, sit on helices S4 and S6, respectively, and their side chains face the cavity. Nearby, several water molecules bound by hydrogen bonds are observed, which may be consumed in the hydrolysis reaction. The cavity has a V-shaped gate open to the lateral direction, but it is usually closed with the L1 loop (Fig. 2). According to the literature [1], it is assumed that upon the approach of a type I transmembrane helix as a substrate L1 undergoes conformational change to accommodate the substrate helix into the cavity. Then, a part of the helix within the cavity unwinds to be cleaved by the hydrolysis.

Protein Data Bank (PDB)

References

Source

  1. Wang, Y. , Zhang, Y. , Ha, Y.; "Crystal structure of a rhomboid family intramembrane protease."; Nature; (2006) 444:179-180 PubMed:17051161.

Others

Author: Ken Nishikawa


Japanese version:PDB:2ic8